LD analysis for SNPs in a list in plink2

[Ethan Kreuzer]

Hi! 

I have list of SNPs and I would like to find proxies for them by finding SNPs in LD with my "ld-snp-list". Currently, it works on plink1.9. (my --keep argument is to specify a sub-ancestry). Here is my code:

"

echo "proxy: Running PLINK LD analysis for chromosome ${CHROM}." > /dev/stderr

Plink1.9/plink --bfile "${PLINK_REF_PANEL}"/"${CHROM}" \

    --r2 \

            --ld-window 1000000 \

            --ld-window-kb 1000 \

            --ld-window-r2 ${PLINK_MIN_R2} \

    --keep "${PLINK_REF_PANEL_KEEP}" \

    --out ${SNAPTMP}/SNAP.${CHROM}.proxy \

    --ld-snp-list ${SNAPTMP}/SNAP.input.proxy \

"

I would like to convert this code to plink2, as I was informed there could be performance benefits as plink2 can use multiple cores. Plink2 does not seem to support this exact command I currently have, so I would like to figure how to do this in plink2. If you also have thoughts on a better way to do this, please let me know! I see there are commands like "--indep-pairphase", "---indep" and "--indep-pairwise", should I be using these commands instead of what I currently have? Please let me know! Thank you

[Christopher Chang]

This isn't a perfect fit for --indep-pairwise, and the other major LD commands haven't been reimplemented in plink2 yet, so you should just continue using plink 1.9 here for now; sorry about the inconvenience.